You hear it before you see it — a roar like a factory in full production. But instead of cars or washing machines, this factory produces scientific knowledge.

Stampede, the newest supercomputer at the Texas Advanced Computing Center (TACC) and one of the most advanced scientific research instruments in the world, fills aisle after aisle of a new 11,000-square-foot data center on the J.J. Pickle Research Campus. Through the glass machine room doors, you can see 182 racks holding more than 500,000 interconnected computer processors. Inside, wind whips from in-row coolers, wires snake over the racks and chilled water courses below the floor as Stampede performs calculations on behalf of scientists and engineers nationwide.

Stampede Research Bits

Check out examples of research already underway using Stampede’s supercomputing power.

Researchers in the social sciences, digital humanities and arts are using Stampede to enable new discoveries. Stampede provides high-performance computing and large-scale visualization to sound archivists to help them search for patterns and gain insights into spoken language and music.

Over the past year TACC staff designed, built and deployed Stampede, working closely with Dell and Intel engineers and university researchers. TACC and The University of Texas at Austin competed against the top supercomputing centers and universities to claim one of the most advanced systems in the world — and won. The award was funded by the National Science Foundation (NSF) with an estimated investment of more than $50 million over a four-year period. The project may be renewed in 2017, which would enable four more years of open science research.

According to the November 2012 Top 500 list of supercomputers, Stampede is the seventh-most powerful advanced computing system on the planet and the most powerful in the U.S. dedicated to academic research, capable of outperforming 100,000 home computers.

On Wednesday, March 27, leaders from government, academia and industry, including The University of Texas at Austin’s President Bill Powers, Jay Boisseauof TACC, Marius Haas of Dell, Diane Bryant of Intel, Farnam Jahanian of the NSF and U.S. Congressman Lamar Smith, will dedicate Stampede and kick off a new era of advanced computing at the university and nationally.

“This is a proud moment for The University of Texas,” President Powers says. “Stampede will serve UT and the nation as it enables scientific exploration that would not otherwise be possible, and it continues TACC’s tradition of providing powerful, comprehensive and leading-edge advanced computing technologies to the open science community.”

As its name suggests, Stampede harnesses the power of a half-million computer processors and combines them to tackle ever larger and more challenging computational problems. Sixteen times more powerful than the recently decommissioned Ranger system (which was most recently ranked as the 50th-fastest supercomputer in the world), Stampede will enable scientists to address new classes of problems they’ve never been able to approach before.

“How often does a scientist get an instrument that’s an order of magnitude more powerful than the one it replaces?” says Omar Ghattas, the John A. and Katherine G. Jackson Chair in Computational Geosciences. “It’s a massive step.”

In recent years, supercomputers have become critical general-purpose instruments for conducting scientific research. Known as the “third pillar” of science, computer simulations and models complement theory and experimentation and allow researchers to explore phenomena that cannot be captured via observation or laboratory experiments.

Supercomputers also allow scholars to mine massive databases of information for digital needles-in-haystacks that otherwise would go unnoticed — such as subtle changes in DNA or the signs of a newly discovered galaxy in a far corner of the universe.

Closer to home, the weather report you checked before going outside, the car you drove to work, the flu shot that protected you from illness — all of these were, at least in part, designed, improved or predicted by a supercomputer.

The reason supercomputers are so important is simple: The universe is governed by mathematical equations, and computers can solve these equations far faster than humans. Enormous supercomputers, like Stampede, enable researchers to solve scientific problems that humans alone would find impossible — the kind that help predict where a hurricane will make landfall, how a new drug will interact with its target, or what mutations in our genetic code make us prone to developing certain diseases.

Stampede acts as a “computational microscope” that allows scientists to explore the inner dynamics of the cell better than with the best imaging devices; helps astronomers peer deeper into the universe’s past than is possible with the most powerful telescopes; enables researchers to develop new materials to remove CO2 from the atmosphere; identifies brain tumors more accurately; and discovers new medicines faster and less expensively than in a laboratory. Stampede will even help researchers in the digital arts and humanities study literature and music in ways they never imagined before.

In the past, supercomputers were often used for a small subset of science and engineering problems. But systems like Stampede, with its comprehensive capabilities, allow many more users to simulate, visualize, analyze, store and share their knowledge with others around the world.

In the first three months of operations, approximately 600 projects and more than 1,200 scientists have used Stampede, which came online in January 2013. These include top researchers in every field of inquiry from mechanical engineering to linguistics to neuroscience. In its lifetime, Stampede is expected to deliver the equivalent of more than 400,000 years of computing to tens of thousands of scientists. Imagine the results Stampede will enable across all fields of knowledge.

Electronic charge rearrangement due to formation of an interface between a thin oxide layer and a ferroelectric PbTiO3 substrate with (a) positive and (b) negative polarization perpendicular to the interface. Due to the positive (negative) substrate polarization, the oxygen atoms (red spheres) at the surface lose (gain) electrons. As a result, CO2 strongly adsorbs to the surface shown in (a), but does not bind to the surface shown in (b).

The Tower at the University of Texas at Austin will shine orange the evening of Friday, June 29, to celebrate the UT robot soccer team’s winning the RoboCup Standard Platform League World Championships in two divisions.

Though the competition is fun, the AI research that is required to compete could someday lead to enhanced bomb-searching robots; autonomous cars that increase traveling efficiency and reduce automobile accidents; self-healing, smart computers; and AI agents that manage business supply chains more effectively than humans.

For the first time in university history, the Texas team also won the RoboCupSoccer Standard Platform League (SPL) competition — one of the highest profile leagues at RoboCup.

RoboCupSoccer SPL consists of teams using state-of-the-art, fully autonomous, humanoid Nao robots. Because the robots are standardized, teams concentrate on software development and programming the robots to “think” and play the game.

“I’m incredibly proud of the students for the great work that they put in, and especially the great research behind the success that made it all possible,” said Stone, a professor in the Department of Computer Science.

The UT Austin Villa RoboCup Team (pink) playing at the 2012 Robot Soccer World Cup in Mexico City.

The Texas SPL team blew through its first round robin games and quarterfinal, winning each by at least a 4-goal margin, and won a nail-biter in the semifinals to go on to compete against the University of Bremen in Germany, the undefeated champions three years in a row. In the championship game, the Texas team took on an early 2-0 lead in the first half, claiming victory by a final score of 4-2.

Inspired by the paper-folding art of origami, chemists at The University of Texas at Austin have developed a 3-D paper sensor that may be able to test for diseases such as malaria and HIV for less than 10 cents a pop.

Such low-cost, “point-of-care” sensors could be incredibly useful in the developing world, where the resources often don’t exist to pay for lab-based tests, and where, even if the money is available, the infrastructure often doesn’t exist to transport biological samples to the lab.

“This is about medicine for everybody,” says Richard Crooks, the Robert A. Welch Professor of Chemistry.

One-dimensional paper sensors, such as those used in pregnancy tests, are already common but have limitations. The folded, 3-D sensors, developed by Crooks and doctoral student Hong Liu, can test for more substances in a smaller surface area and provide results for more complex tests.

]]>http://www.utexas.edu/know/2012/06/01/origami_opad/feed/5Army focuses on university researchhttp://www.utexas.edu/know/2012/03/15/army_westphal_research/
http://www.utexas.edu/know/2012/03/15/army_westphal_research/#commentsThu, 15 Mar 2012 15:50:57 +0000University Communicationshttp://www.utexas.edu/know/?p=24442The United States Army has strong ties to The University of Texas at Austin in research and in officer training.

Undersecretary of the Army Joseph W. Westphal came to campus looking to make those relationships even stronger.

Undersecretary of the United States Army Joseph W. Wesphal (center) visited The University of Texas at Austin campus and met with researchers in neuroscience and energy, as well as Texas Army ROTC cadets and members of the Senior Service College Fellows.Photo: Marsha Miller

Westphal, the second-highest-ranking civilian official in the Army, visited the university March 8 and got a taste of research in neuroscience and energy — areas of concern for the Army and other branches of the armed forces. He also met with members of the university’s Reserve Officers’ Training Corps (ROTC).

Texas was the first of several stops Westphal hopes to make at universities during his tenure as undersecretary.

Westphal is not a stranger to academic life. He was chancellor of the University of Maine System and a political science professor at the University of Maine. He also was provost and professor at the New School in New York City and a faculty member at Oklahoma State University.

The University of Texas at Austin has had a long research relationship with the Department of Defense and the U.S. Army. The Army sponsored an average of $13.6 million in research at the university during the past three years.

Besides research, the university has also provided the Army with its chief scientist. Scott Fish, director of the university’s Institute for Advanced Technology, has served as the Army’s top science adviser since 2010.

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Westphal said the goal of his campus visit was to get a better idea of the resources the university has to offer the Army.

“Whether it’s in engineering, health-related fields, business administration, all of those things give me a flavor,” he said. “This is a first visit to explore that.”

Westphal said he appreciated the spirit of collaboration between the university’s researchers.

“It might be a function of your size and your capacity, but the fact that you’ve got multiple fields working and collaborating in cutting-edge research is something I walk away with pretty impressed,” he said. “And it’s what we look for, that kind of synergy in different disciplines. They’re all integrated in some ways. And I saw that as I went through some of the research examples of the work being done here.”

Neuroscience research is of particular interest to the Army because of the number of veterans returning from Iraq and Afghanistan with post-traumatic stress disorder and traumatic brain injury.

“A lot of our soldiers are exposed to potential brain injury,” Westphal said. “They’ve been in an explosion. They’ve been in an attack. They may not think themselves to have been injured dramatically, physically. They say they’re OK and they look OK, but there might be something wrong.”

Finding out whether something is wrong and how to treat it are problems that university researchers are already grappling with, which is why Westphal’s campus tour started with the new Imaging Research Center in the basement of the Norman Hackerman Building.

The centerpiece of the center is a new magnetic resonance imaging machine, the latest in the technology, according to Jeffrey J. Luci, research assistant professor and manager of the scanner.

The center takes a multilevel and collaborative approach toward understanding memory, traumatic brain injury, development of epilepsy and Alzheimer’s disease.

The tour included the labs of Kristen Harris, a leading expert in electron microscopy; Ila Fiete, a computational biologist; Alison Preston, who studies human episodic memory; Helmut Koester, who uses high-speed lasers to study neuronal circuits; Michael Mauk, who studies working memory at the circuit and behavioral levels; and Kimberly Raab-Graham, who researches the molecular basis of learning and memory and neurodegenerative diseases.

“The Army, as well as all the services, is looking at how we can become more energy efficient, how we can protect the environment in a more significant fashion, how we can address our security issues in respect to energy,” said Westphal, who was briefed on several energy projects at the university.

Westphal was particularly interested in a microgrid project that is developing a simulated model of a military base that would use renewable energy sources so that it could disconnect from the local utility if necessary.

The project, led by John Herbst, a researcher at the university’s Center for Electromechanics, has addressed issues such as the availability of renewable resources and amounts of energy storage needed to run a military installation.

“What we’re trying to do is give you the tools to lay out a long-term plan to upgrade your infrastructure to give you that flexibility … that will allow you to address these (issues),” Herbst said to Westphal.

Westphal asked Herbst to send him a copy of the project’s final report.

Westphal greets Global Policy Studies graduate student Noah Koubenec during a group discussion with other Texas Army ROTC cadets and Senior Service College Fellows.Photo: Marsha Miller

The last stop of Westphal’s visit was a gathering with members of the university’s ROTC program.

He said education in a university setting where there’s a clash of ideas and a high degree of diversity is important to developing capable young officers.

“We’ve given more responsibility to our young leaders whether they are officers or enlisted,” he said. “With that leadership we need a better-educated soldier in the future, at all levels.”

Westphal said he hopes ROTC students learn from a variety of faculty members, especially those who are experts in their fields.

“First and foremost, these institutions are about the next generation of people, and that is about teaching, whether you do it in a research lab or you do it in a classroom,” he said. “And that’s what I want to see for our soldiers. I prefer a well-educated, rounded soldier to be the next leader rather than someone who’s just trained in military tactics.”

]]>http://www.utexas.edu/know/2012/03/05/tanya_paull_cprit_cancer_research/feed/0Extinguishing fearhttp://www.utexas.edu/know/2011/11/10/ptsd_telch_lima/
http://www.utexas.edu/know/2011/11/10/ptsd_telch_lima/#commentsThu, 10 Nov 2011 19:55:53 +0000University Communicationshttp://www.utexas.edu/know/?p=22233The war in Iraq is drawing to a close. But for many servicemen and women, the conflict is far from over. Haunted by images of roadside bombs, ambush attacks and firefights, military personnel suffering from Post Traumatic Stress Disorder (PTSD) are forced to relive their most horrifying wartime experiences.

The severe anxiety disorder is estimated to afflict 11 percent of returning Afghanistan veterans and 20 percent of soldiers who fought in Iraq, according to the U.S. Department of Veterans Affairs. Symptoms include flashbacks, an excessive startle response, depression, anxiety and sleep disorders.

To lessen the time it takes for PTSD patients to recover from these debilitating ailments, University of Texas at Austin psychology professors Michael Telch and Francisco Gonzalez-Lima, along with their team of researchers, are pairing a memory-enhancing drug with prolonged exposure therapy.

In prolonged exposure therapy, patients repeatedly recount the memory of the traumatic event. As therapy progresses, the fear of the memory weakens and patients begin to feel more in control of their emotions and their lives in general. Typically about two thirds of PTSD patients treated with prolonged exposure therapy during 10 90-minute sessions no longer exhibit PTSD.

“There is now compelling scientific evidence demonstrating exposure therapy to be effective in the treatment of PTSD, however there is still a clear need to make the treatments work better and faster,” says Telch, professor of psychology.

The researchers believe the FDA-approved compound USP methylene blue, which significantly improved fear extinction in rats in an earlier study conducted in the Gonzalez-Lima Lab, will help strengthen the extinction of fear that occurred during prolonged exposure therapy sessions.

As part of the animal study, Gonzalez-Lima and his research team subjected rats to fearful stimuli during a fear extinction session, then administered USP methylene blue. With the drug,
Gonzalez-Lima said they were able to significantly reduce the rats’ fears.

“USP methylene blue is an effective therapeutic intervention in animal models of neuropsychiatric disorders, including PTSD,” says Gonzalez-Lima, professor in the Department of Psychology and the College of Pharmacy. “The drug’s potential to enhance fear extinction may serve as an adjunct to psychotherapy, as a novel way to improve exposure therapy outcome for anxiety disorders.”

After successfully achieving positive results from the rat study, the researchers are taking the next important step by testing whether the drug enhances fear extinction in PTSD patients undergoing exposure therapy.

Professor Francisco Gonzalez-Lima is a world leader in research that investigates the relationship between brain metabolism, learning and memory. Photo: Marsha Miller

As part of the study, conducted in Telch’s Laboratory for the Study of Anxiety Disorders and at two other sites, the University of Washington and the University of Pennsylvania, respondents take a placebo pill or a dose of the drug after a therapy session. The researchers theorize the patients taking the medication will recover faster and better in only six daily one-hour sessions.

“We are hopeful the promising findings of Dr. Gonzalez-Lima and others, showing that USP methylene blue enhances the extinguishing of fear in rodents, will carry over to exposure therapy in humans, and thus provide a safe and convenient method for enhancing exposure therapy for PTSD and possibly other anxiety disorders as well,” says Telch.

Post-traumatic stress symptoms often emerge immediately after traumatic experiences. For most, these symptoms subside on their own soon after the trauma. However, about 30 percent of trauma victims go on to develop PTSD in which their trauma memories continue to haunt them and create significant distress and life impairment for months or years after the event.

As patients repeatedly recount a frightening event in prolonged exposure therapy, they begin to look at the memory differently. The researchers predict USP methylene blue will expedite this process, saving the patients both time and medical expenses.

“We predict that patients given a memory boost with USP methylene blue immediately after therapy sessions will make more lasting gains during therapy than those who do not take the medication,” Telch says.

Taken orally, the chemical properties of USP methylene blue affect regions of the brain, such as those mediating fear extinction.

“Methylene blue easily crosses the blood-brain barrier and accumulates inside activated brain cells,” Gonzalez-Lima says. “Once inside the neurons, the substance zooms in on mitochondria – the power house of the cell – to keep it active and enable the brain cells to keep processing the memory.”

The researchers are recruiting participants for the study, which is a clinical trial funded by the National Institute of Mental Health, conducted in the Laboratory for the Study of Anxiety Disorders at The University of Texas at Austin. For more information about participating in the study, call 512-404-9118.

In 2009 the National Science Foundation (NSF) funded a five-year interdisciplinary study at The University of Texas at Austin to address the growing debate about the effects of microwave radiation. After two years, Electrical & Computer Engineering Assistant Professor Ali Yilmaz and his colleagues have built one of the highest-resolution electromagnetic human models to date: AustinMan. The model is helping to determine the effects of microwaves from wireless devices on the body.

“You have all these bright future pictures of connectedness and then all these scare stories telling you to turn off your cellphones,” said Yilmaz. “What are the effects of all these nearby wireless devices on us?”

]]>http://www.utexas.edu/know/2011/10/17/austinman/feed/0Doctoral student works to diagnose hearing impairments in childrenhttp://www.utexas.edu/know/2011/07/22/hsieh_csd/
http://www.utexas.edu/know/2011/07/22/hsieh_csd/#commentsFri, 22 Jul 2011 17:59:13 +0000Samantha Youngbloodhttp://www.utexas.edu/know/?p=20659This story originally appeared in On the Record, a publication of the College of Communication.

After Michelle Hsieh greets her research participants in the lobby of the Speech and Hearing Center in the College of Communication, she escorts them to a tiny room at the back of the clinic.

The room contains towers of electronic equipment with red blinking lights, wires threading along the floor and walls, and a giant steel chamber that looks like a bank vault with a window.

Inside the chamber — called a sound booth — Hsieh seats participants in a maroon recliner. After fitting them with earphones, she attaches electrode sensors to various points on their heads.

For two hours, she plays a succession of sounds — oscillating beeps that resemble a toad croaking — and asks them to remain motionless. She sits close by studying the readings from the sensors on her computer.

Hsieh pays her research participants — normally undergraduate students — $10 an hour to listen to specific sounds while she analyzes their brainwaves. “You play sounds into their ears, and sound generates neural activ­ity,” said Hsieh. “Neurons will fire in a predictable way in response to that sound, and you can measure the response via the electrodes and know what it’s supposed to look like, and obtain information about his or her hearing.”

Hsieh said electrophysiological audiology holds tremendous potential for identifying hearing problems in infants and young children — who can’t participate in normal hearing tests.

In the normal tests, audiologists play specific sounds for patients and ask them to indicate when they’ve heard a sound by raising a hand or pressing a button. If the patient does not respond, the audiologist can tell the patient has a hearing problem.

But what if the patient is an infant or young child and unable to respond to the audiologist? Hsieh said the hearing impairment could go undiagnosed.

Early diagnosis is crucial, so doctors can begin treatment or teaching a child sign language. “A child with a hearing impairment from birth or at a young age due to illness has the chance of not being able to develop language,” she said. “Language is the medium by which we interact with the world. You have to have language to be able to be a productive member of society and have meaningful relationships.”

Currently, she is researching a specific “auditory steady state response” test to help determine how well a person hears timing and pitch. In addition to giving participants the electrophysiological test, Hsieh uses a variation of normal hearing tests — what she calls “behavioral” tests. She then compares the data from the two to see if she can predict how their brainwaves should look.

Her research received the 2011 Student Researcher Investigator Award from the American Academy of Audiology, one of two $5,000 awards given to doctoral students nationally.

Originally from Richardson, Texas, Hsieh dresses casually in jeans and tennis shoes. At 27, she could be mistaken for an undergraduate rather than someone who is working on her second doctorate. When she finishes her Ph.D. in 2012, she will be the first person to earn two doctorates from the CSD department. Her first doctorate was in audiology — called an Au.D. — which enables her to diagnose and treat patients with hearing impairments.

A Ph.D. will enable her to conduct research on the hearing of infants and children, something she be came interested in at Dell Children’s Hospital, where she works part time as an audiologist.

Craig Champlin, the chair of the CSD department and Hsieh’s graduate advisor, said clinical experience can benefit a researcher. “I think it is a great arrangement because she is able to see on a daily basis where the holes exist in our knowledge base,” Champlin said. “She sees a child that needs this test, treatment, intervention or diagnosis that we’ve never seen before, and it’s something that she can study further in the controlled environment of the laboratory.”

In addition to working on her second doctorate, she holds a bachelor’s degree from the CSD department. When she graduates in 2012, she will have spent 10 years as a student at UT.

Hsieh said every semester she studies audiology, she finds it more fascinating. “In healthcare typically, there’s something that goes wrong with your body somewhere, and then there will be a professional who specializes in knowledge of that part,” she said. “What appealed to me about CSD was that what is impaired isn’t just a body part, it’s a way of life. It’s the means by which we interact with our world.”

Editor’s note: This story has been updated to change “A child who is hearing impaired” to “A child with a hearing impairment” in an effort to address the person first and the physical condition second.

]]>http://www.utexas.edu/know/2011/07/22/hsieh_csd/feed/8The dangers of cannibalismhttp://www.utexas.edu/know/2011/07/14/cannibalism/
http://www.utexas.edu/know/2011/07/14/cannibalism/#commentsThu, 14 Jul 2011 19:36:50 +0000Samantha Youngbloodhttp://www.utexas.edu/know/?p=20563Andy Ellington studies RNA, the origins of life, synthetic biology and develops therapeutics. He is a research professor in the Department of Chemistry and Biochemistry and the Institute for Cellular and Molecular Biology. This story originally appeared on Ellington’s blog and can also be read on the Texas Science Web site.

Cannibalism. One of the last, great taboos. And for good biological reasons. In the Eastern Highlands of Papua New Guinea the locals, known as the Fore, practiced what was politely called “transumption,” which led during the late 1950s to the person-to-person transmission of a debilitating disease, kuru, in epidemic proportions. The “laughing disease” led to massive neural degeneration, eventually resulting in death (although sometimes with long latency periods), and was the result of the transmission of prions.

Prions are interesting because they’re sort of the exception that proves the rule of DNA. That is, while DNA replicates sequence, prions replicate conformation. Prions are peptides or proteins that assume a particular conformation. When a prion comes in contact with a similar protein that is not shaped the same the prion forces the protein to assume its conformation, and they aggregate together in a tight knit architecture known as an amyloid. This is the same sort of amyloid that occurs in the very similar prion disease Creutzfeld-Jakob disease (CJD) and in Alzheimer’s. So, you can sort of think of prions as the first domino that initiates a cascade of conformational events that leads to a big, tangled mess in your brain. Not good.

Here’s what’s been making me think. There is a variant of CJD (vCJD) that arose a few years ago in England and that could be traced, roughly, to the widespread distribution of what Denny Crane would call “the mad cow disease,” but which is more commonly known as Bovine Spongiform Encephelapathy. Here’s what I find fascinating: you feed cows the remains or waste of other cows, BSE can spread like wildfire (and who can forget the giant bonfires of cows in England circa the late 1980s). But while there were upwards of 180,000 cases of BSE amongst cows, there were only about 153 cases of vCJD (Beghi et al. (2004), Neurol Sci 25:122). The causal link between BSE and vCJD is sort of like the causal link between human activity and global warming: pretty convincing evidence, but hard to definitively prove (and in both cases the appropriate experiments that might directly test the hypotheses are understandably hard to run).

These round, packed deposits of abnormal prion protein are known as florid plaque. They often form in the brains of people suffering from variant Creutzfeld-Jakob disease (vCJD).

Some folks think that the low transmission rates from cows to humans just hide an epidemic-to-come in which those of us who consume multiple hamburgers per day (what?) will eventually twitch out. But it is more likely that there are huge species barriers in prion replication. This is because at the molecular level a cow prion may only partially recognize and bind to the amino acid sequence in the corresponding normal human protein, inhibiting the kicking over of that first domino (Priola (1999), Biomed Pharmacother 53:27).

This presumed species barrier is confirmed by experiments with prion transmission in test tubes, cells, and transgenic mice. Thus, cow-on-cow or human-on-human chomping is a much more likely route to disease than humans eating cows (or whatever happens in the future on the Gary Larson-esque “Planet of the Cows“).

So, what are the implications of this understanding? Clearly, don’t eat people, soylent or not. Indeed, the depth of the taboo suggests that our species may have discovered this edict several times over in our past (and there is even a serious-but-unlikely hypothesis that cannibalistic Neanderthals succumbed to spongiform encephalopathies). Keep your factory farms clean. Amusingly, many of the bans on beef that accompanied the outbreak of BSE in England (and more minor outbreaks in the US) were more political than practical.

But I think there’s also a more fundamental issue. While spongiform encephalopathies seem to focus on a relatively small number of neurologically important proteins, a surprisingly huge number of proteins can form amyloids. Indeed, work from the Marcotte lab down the hall (with a small assist from our own lab) has revealed that a surprisingly large number of yeast proteins (like, 30 percent, of all proteins) seem to self-aggregate. To the extent that those aggregates are amyloids this would mean that there are many dominoes waiting to fall. Why don’t they? Well, most proteins inside of cells are disentangled by energy-burning so-called chaperones (and, indeed, the prion protein that falls down is on the *outside* of cells in the brain).

Indeed, the fact that we’re not cannibals means we don’t know much about these other dominos. Or, to put it another way, prions are a growth industry from a biodefense point of view. How many different human peptides, available orally, just like kuru was, would inevitably take down large fractions of a population after a suitably long and stealthy incubation period? And given the concerns I’ve previously noted about the quality controls in our supply chains (see “On Pepcid,” which incidentally is back on the shelves, woo hoo!), would such prions be relatively easy to introduce (think melamine)? And unlike viral or microbial diseases, where we at least have a basal understanding of how to construct a biodefense, there really is no defense against prions (just as, sadly, there is no real cure for Alzheimer’s). The suggested procedures for prion researchers to decontaminate their workspaces and tools involve essentially treating everything with the most caustic agents you can imagine. That’s not going to work for your brain. And so I am left once again with a conclusion that is an unsatisfying bummer: we’re hosed. Unless the same cultural prohibitions that keep us from eating one another kick in with respect to infecting one another. The thin, nice line. Quaint.

]]>http://www.utexas.edu/know/2011/07/14/cannibalism/feed/14Conquering breast cancerhttp://www.utexas.edu/know/2011/06/28/zhang_cancer_research/
http://www.utexas.edu/know/2011/06/28/zhang_cancer_research/#commentsTue, 28 Jun 2011 18:37:06 +0000Samantha Youngbloodhttp://www.utexas.edu/know/?p=20346This story originally appeared on the Cockrell School of Engineering Web site.

Breast cancer affects nearly one out of eight American women during their lifetime. Of those women, around 40 percent undergo more than one surgery to remove malignant breast tissue.

Dr. John Zhang wants to change these odds — and his solution includes biopsy-free examinations and real-time pathology imaging during surgery.

“Cancer is the top disease that is killing people,” said Zhang, a professor in the Department of Biomedical Engineering at the Cockrell School. “And right now, we know biopsy is the standard. Doctors are removing tumors in the breast without having anything to tell them if the whole tumor has been removed … patients wait through a 24-hour time cycle to learn whether the cancer tumor is still there.”

Zhang’s new technology eliminates the wait.

He has developed a new technology that acts like a GPS device for cancer surgeons. The instrument guides doctors during surgery, enabling them to see in real time whether all of the cancerous tissue has been removed.

According to Zhang, the key innovation behind the technology is a micro-electro-mechanical system (MEMS) laser scanner. This handheld device — which uses a microchip that was created in his lab — generates real-time 3-D images of surface cell tissue, or more technically, ‘confocal images of epithelial tissue.’

While confocal imaging has been around for a few decades, miniaturized confocal imaging devices — such as the handheld one Zhang has developed with his laser microchip technology — are something new.

The main method to generate confocal images is to use a large-scale microscope that costs more than $1 million and requires a biopsy from the patient.

In contrast, Zhang’s technology “brings the microscope to the patient, not the tissue to the microscope.”

“Fundamentally, this chip would enable a new platform that integrates very small and cost effective components replacing the large device,” he said.

Zhang started researching real-time imaging devices for early cancer detection in 2006, and has continued to receive funding from the National Science Foundation, National Institute of Health (NIH), National Instruments and others.

“I think that it’s really important for the technologies developed at top engineering schools to make an impact on society,” he said. “We are using federal support and tax dollars, so we should work very hard to improve the quality of life. I really want to bring research to society.”

Recently, Zhang received nearly $1 million from NIH’s National Cancer Institute to fund his research initiatives over the next three years. Collaborators include Dr. Kostia Sokolov, adjunct associate professor of biomedical engineering, and Drs. Eugene Frenkel and Jonathan Uhr, professors of internal medicine and radiology at UT Southwestern Medical Center in Dallas.

The team also includes biomedical engineering graduate student Youmin Wang and undergraduate student Milan Raj.

“We have very talented students and they want to solve societal problems and conquer cancer,” Zhang said. “We do this discovery every day in the lab and that is part of the learning and the education — the knowledge moving forward.”

This forward momentum inspired Zhang to license his microchip technology with the university’s Office of Technology Commercialization, and create a spin-off company called NanoLite Systems Inc. The company was co-founded with Ting Shen who received her Ph.D. from Stanford University and later worked for McKinsey & Co. and Cisco Systems, but left to become CEO of NanoLite.

“If we can take this [technology] to market and reduce that redo rate for cancer surgery by just a few percent, we are moving the needle in a lot of people’s lives,” Shen said.

Shen was immediately inspired by Zhang’s research and the impact it could have on breast cancer detection, noting she has had close friends and family diagnosed with cancer.

“I’ve heard real life stories from patients — they anxiously await the call from the doctor to see if they are cancer free now. It’s emotionally and physically painful,” she said. “If we have the technology to develop cancer imaging devices that enable doctors to see better — to see cancer in real time during surgery — then they can remove the cancer much better.”

NanoLite Systems is currently working with the Austin Technology Incubator to help commercialize the technology and propel the company’s success. Shen recently presented the business plan at the Texas Venture Labs Expo during Venture Week.

“This technology started here at UT Austin and we will contribute to the vision to conquer cancer, in Texas [and] in Austin,” Zhang said. “If we aren’t doing it here, somewhere else will.”